Federal officials say they have overly criticized, and in many cases penalized, Medicare health plans for serious deficiencies, including the improper rejection of claims for medical services and unjustified limits on coverage of prescription drugs.

The findings, cataloged in dozens of federal audit reports, come as millions of older Americans sign up for private health plans and prescription drug plans in Medicare’s annual open enrollment period, which began on Wednesday, October 15 and continues through December 7.

About 16 million people, accounting for 30 percent of the 54 million beneficiaries, are in private Medicare Advantage plans, which provide a full range of health care services under contract with the government. An additional 23 million people are in prescription drug plans, which cover only medications.

Federal officials expressed frustration that they were seeing the same kinds of deficiencies year after year. In a memorandum to health plans, Gerard J. Mulcahy, the Medicare official in charge of oversight and enforcement, listed common “areas of noncompliance” identified in program audits.

Medicare officials impose civil fines and take other enforcement actions when they see practices that could harm beneficiaries by delaying or denying access to care. Insurers usually do not dispute the audit findings, but say the care they provide is superior to that in the traditional fee-for-service Medicare program.

The Centers for Medicare and Medicaid Services reported these findings:

In more than half of all audits, “beneficiaries and providers did not receive an adequate or accurate rationale for the denial” of coverage when insurers refused to provide or pay for care.

When making decisions, insurers often failed to consider clinical information provided by doctors and failed to inform patients of their appeal rights.

•In 61 percent of audits, insurers “inappropriately rejected claims” for prescription drugs. Insurers enforced “unapproved quantity limits” and required patients to get permission before filling prescriptions when such “prior authorization” was not allowed.

Medicare plans frequently missed deadlines for making decisions about coverage of medical care, drugs and devices requested by doctors and patients.

Several companies have been penalized in the last year for violations, including Medicare’s patient-protection requirements, officials said.

John K. Gorman, a former Medicare official who is a consultant to many insurers, said, “It’s unforgivable that so many Medicare Advantage plans are still struggling with basic compliance issues.”

Insurers often hire companies to manage their drug benefits. “These companies know how to manage drug benefits for working-age people with commercial insurance, but they are confounded by the complex needs of seniors,” Mr. Gorman said. “Many are failing Medicare beneficiaries.”

Federal officials have begun to inform some companies this year that they could not enroll any more Medicare beneficiaries and should stop marketing their Medicare plans.

Mr. Mulcahy, the Medicare official, said the conduct of these companies “poses a serious threat to the health and safety of Medicare beneficiaries.”

“Violations resulted in enrollees experiencing delays or denials in receiving prescription drugs,” Mr. Mulcahy said, also citing the companies for “inappropriate denials of payment for emergency medical services.”

Spokespersons from these companies said they are taking “these matters very seriously” and are trying to fix the problems so the sanctions can be lifted.

The Obama administration has imposed civil penalties of more than $500,000 on one of the companies, saying it found “widespread and systemic failures” in the management of prescription drug benefits for Medicare patients.

“This company failed to provide its enrollees with benefits” in accordance with Medicare requirements, Mr. Mulcahy said in a letter to the insurer. But, a spokeswoman for the company, said the problems “involved administrative issues, not quality, and have long since been resolved.”

In a letter to another California insurer, the federal government said it had discovered “multiple serious violations on almost all files reviewed” in its audit of the company’s Medicare plan.

The severity of this California insurer’s conduct is magnified by the fact that more than 99 percent of its enrollees are beneficiaries who receive the low-income subsidy,” Mr. Mulcahy wrote.

The chief executive of this California company, a nonprofit health plan, said, “We did not disagree with any of the findings about unnecessary delays and inappropriate denials of care.” Many of the problems, he said, resulted from inadequate supervision of the physician networks and its pharmacy-benefits manager.

This California insurer said it was making improvements but could not enroll new Medicare beneficiaries until the government was satisfied that the deficiencies had been corrected.

Federal officials imposed a $180,400 penalty on a company after finding that it improperly restricted access to certain prescription drugs.  The spokeswoman for this insurer, said, “We did not dispute the findings.” The company has paid the penalty and corrected the deficiencies, she said.

An Oregon insurer paid a penalty of $312,300 for violations involving drug benefits, coverage decisions and the handling of consumer complaints. “This is the first time this has ever happened to us,” said a vice president of the company. “We’ve quickly done everything that Medicare asked of us.”